This invention relates to methods for concurrently performing multiple biological chip assays. The invention therefore relates to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine and diagnostics.
New technology, called VLSIPS(trademark), has enabled the production of chips smaller than a thumbnail that contain hundreds of thousands or more of different molecular probes. These biological chips or arrays have probes arranged in arrays, each probe assigned a specific location. Biological chips have been produced in which each location has a scale of, for example, ten microns. The chips can be used to determine whether target molecules interact with any of the probes on the chip. After exposing the array to target molecules under selected test conditions, scanning devices can examine each location in the array and determine whether a target molecule has interacted with the probe at that location.
Biological chips or arrays are useful in a variety of screening techniques for obtaining information about either the probes or the target molecules. For example, a library of peptides can be used as probes to screen for drugs. The peptides can be exposed to a receptor, and those probes that bind to the receptor can be identified.
Arrays of nucleic acid probes can be used to extract sequence information from, for example, nucleic acid samples. The samples are exposed to the probes under conditions that allow hybridization. The arrays are then scanned to determine to which probes the sample molecules have hybridized. One can obtain sequence information by careful probe selection and using algorithms to compare patterns of hybridization and non-hybridization This method is useful for sequencing nucleic acids, as well as sequence checking. For example, the method is useful in diagnostic screening for genetic diseases or for the presence and/or identity of a particular pathogen or a strain of pathogen. For example, there are various strains of HIV, the virus that causes AIDS. Some of them have become resistant to current AIDS therapies. Diagnosticians can use DNA arrays to examine a nucleic acid sample from the virus to determine what strain it belongs to.
Currently, chips are treated individually, from the step of exposure to the target-molecules to scanning. These methods yield exquisitely detailed information. However, they are not adapted for handling multiple samples simultaneously. The ability to do so would be advantageous in settings in which large amounts of information are required quickly, such as in clinical diagnostic laboratories or in large-scale undertakings such as the Human Genome Project.
This invention provides methods for concurrently processing multiple biological chip assays. According to the methods, a biological chip plate comprising a plurality of test wells is provided. Each test well defines a space for the introduction of a sample and contains a biological array. The array is formed on a surface of the substrate, with the probes exposed to the space. A fluid handling device manipulates the plates to perform steps to carry out reactions between the target molecules in samples and the probes in a plurality of test wells. The biological chip plate is then interrogated by a biological chip plate reader to detect any reactions between target molecules and probes in a plurality of the test wells, thereby generating results of the assay. In a further embodiment of the invention, the method also includes processing the results of the assay with a computer. Such analysis is useful when sequencing a gene by a method that uses an algorithm to process the results of many hybridization assays to provide the nucleotide sequence of the gene.
The methods of the invention can involve the binding of tagged target molecules to the probes. The tags can be, for example, fluorescent markers, chemiluminescent markers, light scattering markers or radioactive markers. In certain embodiments, the probes are nucleic acids, such as DNA or RNA molecules. The methods can be used to detect or identify a pathogenic organism, such as HIV, or to detect a human gene variant, such a the gene for a genetic disease such as cystic fibrosis, diabetes, muscular dystrophy or predisposition to certain cancers.
This invention also provides systems for performing the methods of this invention. The systems include a biological chip plate; a fluid handling device that automatically performs steps to carry out assays on samples introduced into a plurality of the test wells; a biological chip plate reader that determines in a plurality of the test wells the results of the assay and, optionally, a computer comprising a program for processing the results. The fluid handling device and plate reader can have a heater/cooler controlled by afthermostat for controlling the temperature of the samples in the test wells and robotically controlled pipets for adding or removing fluids from the test wells at predetermined times.
In certain embodiments, the probes are attached by light-directed probe synthesis. The biological chip plates can have 96 wells arranged in a rows and 12 columns, such as a standard microtiter plate. The probe arrays can each have at least about 100, 1000, 100,000 or 1,000,000 addressable features (e.g., probes). A variety of probes can be used on the plates, including, for example, various polymers such as peptides or nucleic acids.
The plates can have wells in which the probe array in each test well is the same. Alternatively, when each of several samples are to be subjected to several tests, each row can have the same probe array and each column can have a different array. Alternatively, all the wells can have different arrays.
Several methods of making biological chip plates are contemplated. In one method, a wafer and a body are provided. The wafer includes a substrate and a surface to which is attached a plurality of arrays of probes. The body has a plurality of channels. The body is attached to the surface of the wafer whereby the channels each cover an array of probes and the wafer closes one end of a plurality of the channels, thereby forming test wells defining spaces for receiving samples. In a second method, a body having a plurality of wells defining spaces is provided and biological chips are provided. The chips are attached to the wells so that the probe arrays are exposed to the space. Another embodiment involves providing a wafer having a plurality of probe arrays; and applying a material resistant to the flow of a liquid sample so as to surround the probe arrays, thereby creating test wells.
This invention also provides a wafer for making a biological chip plate. The wafer has a substrate and a surface to which are attached a plurality of probe arrays. The probe arrays are arranged on the wafer surface in rows and columns, wherein the probe arrays in each row are the same and the probe arrays in each column are different.